weightedCor {analogue}  R Documentation 
Weighted correlation test of WA reconstruction
Description
Weighted correlation between WA optima from training set and axis 1 scores of constrained ordination fitted to fossil data with WA model predictions for fossil samples as constraints.
Usage
## Default S3 method:
weightedCor(x, env, fossil, method = c("rda", "cca"),
test = TRUE, type = c("simulate", "permute"), sim = 999,
verbose = TRUE, ...)
## S3 method for class 'weightedCor'
plot(x,
type = c("bubble", "null"),
weighted = TRUE,
size = 0.25,
xlab = paste(x$env, "WA Optima"),
ylab = "Axis 1 Score",
xlim,
main = "",
sub = NULL,
border = "gray75",
col = "gray75",
obscol = "red",
fg = "black", ...)
Arguments
x 
training set covariates, a matrixlike object usually of
species/proxy data. For the 
env 
training set response, a vector usually of environmental data. 
fossil 
matrix of fossil/core species/proxy data for which a reconstruction is sought. 
method 
constrained ordination method. One of 
test 
logical; should the observed correlation be tested? 
type 
the type of test to apply. One of 
sim 
numeric; number of simulations or permutations to permform as part of the test 
verbose 
logical; should the progress of the test be shown via a progress bar? 
... 
arguments passed to other methods. In the case of the

weighted 
logical; should the null distribution plotted be of the weighted or normal correlation. 
size 
numeric; the size of the largest bubble in inches. See

xlim , xlab , ylab , main , sub 
graphical parameters with their usual meaning. 
border , col 
The border and fill colours for the histogram bars. 
fg 
The colour of the bubbles drawn on the bubble plot. 
obscol 
The colour of the indicator for the observed correlation. 
Value
The plot
method produces a plot on the current
device. weightedCor()
returns a list with the following
components:
wtdCorrel , Correl 
numeric; the observed weighted and standard correlation. 
data 
data frame; containing the training set WA Optima, axis 1 species scores, and mean abundance for each species. 
ord 
the fitted constrained ordination. 
model 
the fitted WA model. 
method 
the ordination method used. 
ndist 
the null distribution produced. 
sim 
numeric; the number of simulations or permutations used to test the observed correlations. 
type 
the type of test performed. 
env 
the deparsed version of 
call 
the matched function call. 
Author(s)
Gavin L. Simpson
References
Telford R.J. and Birks, H.J.B. (2011) A novel method for assessing the statistical significance of quantitative reconstructions inferred from biotic assemblages. Quanternary Science Reviews 30:12721278.
See Also
wa
for details on fitting weighted average models.
Examples
data(ImbrieKipp, SumSST, V12.122)
Cor < weightedCor(ImbrieKipp, env = SumSST,
fossil = V12.122, type = "simulate", sim = 49)
Cor
plot(Cor)
plot(Cor, type = "null")